title: 2128_2_C0001_T0001

description:
Control (CH1): Seedlings of 12days old of rice (Oryza sativa L. cv Nipponbare) was soaked in DW and incubated at 29 degreesCf or 12 hours. The seedlings were used for total RNA extraction using RNA easy plant mini kit. Extracted total RNA from the seedlings were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedlings of 12days old of rice (Oryza sativa L. cv Nipponbare) was soaked in soaked in 150mM NaCl and incubated at 29 degreesC for 12 hours. The seedlings were used for total RNA extraction using RNA easy plant mini kit. Extracted total RNA from the seedlings were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Salt, ,

source_name: Control (CH1) source: The root of 12 days old seedlings

source_name: Target (CH2) source: Seedling (12 days old)  treated with 150mM NaCl for 12 hours


title: 2129_2_C0201_T0201

status: Public on Aug 13 2009

type: RNA

city: Tsukuba

first: Shoshi

last: Kikuchi

state: Ibaraki

address: 2-1-2 Kan-nondai

department: Molecular Genetics

country: Japan

institute: National Institute of Agrobiological Sciences

description:
Control (CH1): Maize (Zea mays L. cv. Alice) plant were grown hydroponically at normal condition for 9 day. Root of the plant were harvested on 20 days after sowing for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Maize (Zea mays L. cv. Alice) plant were grown hydroponically at Fe-deficient condition for 9 day. Root of the plant were harvested on 20 days after sowing for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Nutrient, Fe-deficiency , Maize

molecule: total RNA

organism: Zea mays

source_name: Control (CH1) source: Root (at hydroponics for 20 days after sowing) grown  at normal condition for 9 day (control)

source_name: Target (CH2) source: Root (20 days after sowing)  treated with Fe-deficient condition for 9 days


title: 2131_1_C0001_T0001

description:
Control (CH1): Seedlings of rice (Oryza sativa L. cv Nipponbare) were grown at 28 degreesC for 8 days {day 1 to 6 in light, day 7 to 8 (48 hours) in dark} without submerged (0 hour). Shoot part of the plant were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedlings of rice (Oryza sativa L. cv Nipponbare) were grown at 28 degreesC for 8 days {day 1 to 6 in light, day 7 to 8 in dark with submerged condition (48 hours)}. Shoot part of the plant were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Anerobic, ,

organism: Oryza sativa

source_name: Control (CH1) source: 8-day-old shoot of seedling (control)

source_name: Target (CH2) source: 8-day-old seedlings (shoot) submerged for 48 hours


title: 2129_2_C0001_T0001

description:
Control (CH1): Rice plants (Oryza sativa L. cv. Arkansus) were grown hydroponically for 4 week. Then the plants were transferred to MS medium (pH 4.3) including  0 microM Aluminum for 36 hours as control. Root of the plants were harvested for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice plants (Oryza sativa L. cv. Arkansus) were grown hydroponically for 4 week. Then the plants were transferred to MS medium (pH 4.3) including 100 microM Aluminum  for 2 hours after treatment of 0 microM Aluminum for 34 hours. Root of the plants were harvested for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Nutrient, Aluminium,

source_name: Control (CH1) source: Root (cultured hydroponically for 4 week) treated with 0 microM aluminium for 36 hours (control)

source_name: Target (CH2) source: Root (cultured hydroponically for 4 week) treated with aluminium (100 microM, 34 hour)


title: 2124_2_C0001_T0003

description:
Control (CH1): Rice plants (Oryza sativa L. cv. cool-tolerant crossed rice lines #2) were grown on paddy field soil in 1/2000a Wagner pot. 0.9g each of nitrogen, phosphorus and potassium, 0.3g each of magnesium and calcium and trace of iron and manganese were added to the soil. In the cultivation, growth chamber (12L at 26C (300uE/m2/sec); 12D at 20C : relative humidity  75%) was used. Anther early middle microspore stage of the plants (72 day after sowing; -1 to 2 cm of auricle distance; pollen germination pores were examined under a microscope) was used for total RNA extraction by CTAB method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice plants (Oryza sativa L. cv. cool-tolerant crossed rice lines #2) were grown under ordinary greenhouse condition and cooled at 12 degreesC for 5days while the anthers moved from the young microspore stage to the early middle stage. Anthers of the plants at the early middle microspore stage were used for RNA extraction by CTAB method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, ,

source_name: Control (CH1) source: Rice plants (anther early middle microspore stage) were grown under greenhouse condition

source_name: Target (CH2) source: Rice plants (anthers at the early middle microspore stage) treated with low temperature (12 degrees C, 5days)


title: 2133_2_C0002_T0005

description:
Control (CH1): Suspension-cultured cell derived from germinating seed of rice (Oryza sativa L. cv Kakehashi) was incubated for 8 hours in phosphate buffer (pH6.0) added medium. Extracted total RNA from the cell were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Suspension-cultured cell derived from germinating seed of rice (Oryza sativa L. cv Kakehashi) was incubated for 8 hours in blast fungal elicitor and MAPKK inhibitor (PD98059) added medium. Extracted total RNA from the cellwere labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Pathogen, Blast fungal elicitor , MAPKK inhibitor

source_name: Control (CH1) source: Suspension-cultured cell derived from germinating seed incubated for 8 hours

source_name: Target (CH2) source: Suspension-cultured cell incubated for  8 hours in blast fungal elicitor and MAPKK inhibitor (PD) added medium


title: 2124_1_C0001_T0002

description:
Control (CH1): Rice plants (Oryza sativa L. cv. Hayayuki) were grown under ordinary greenhouse condition. Anthers of the plants at the early middle microspore stage were used for RNA extraction by CTAB method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice plants (Oryza sativa L. cv. Hayayuki) were grown under ordinary greenhouse condition and cooled at 12 degreesC for 5days while the anthers moved from the young microspore stage to the early middle stage. Anthers of the plants at the early middle microspore stage were used for RNA extraction by CTAB method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, ,

source_name: Control (CH1) source: Rice plants (anthers at the early middle microspore stage) grown under greenhouse condition.


title: 2126_2_C0101_T0101

description:
Control (CH1): Spikelets (5.5 - 6.5 mm long) with young microspores of rice plants {Oryza sativa L. cv. the chilling tolerant near-isogenic line (B5F5) derived from five backcrosses between a recurrent parent 'Toyohikari' (chilling suceptible) and a donor parent 'Hayayuki' (chilling tolerant)} grown at  25/19 degrees C (day/night) for 4 days in phytotron, were harvested at the early microspore stage (11 days before heading). Harvested spikelets were used for RNA extraction by Fast RNA-kit. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Spikelets (5.5 - 6.5 mm long) with young microspores of rice plants {Oryza sativa L. cv. Toyohikari (chilling susceptible at the booting stage), the recurrent parent of the near-isogenic line '510-2' } grown at  12 degreesC for 1 days, were harvested at the early microspore stage (11 days before heading). Harvested spikelets were used for RNA extraction by Fast RNA-kit. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, ,

source_name: Control (CH1) source: Spikelets with young microspores at the early microspore stage (11 days before heading)

source_name: Target (CH2) source: Spikelets with young microspores treated with low temperature (12 degreesC, 1 days)


title: 2127_2_C0001_T0001

description:
Control (CH1): Callus derived from rice seed (Oryza sativa L. cv Nipponbare) were grown in MS medium with 2,4-D for 24 hours. Then the callus were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Callus derived from rice seed (Oryza sativa L. cv Nipponbare) were grown in MS medium with 2,4-D for 24 hours. The callus were treated with 30 microM methyl jasmonate for 30 min. Then the callus were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Methyl jasmonate ,

source_name: Control (CH1) source: Rice callus (non-treated)

source_name: Target (CH2) source: Callus treated with 30 microM methyl jasmonate for 30 min.


title: 2128_2_C0001_T0003

description:
Control (CH1): Seedlings of 12days old of rice (Oryza sativa L. cv Nipponbare) was soaked in DW and incubated at 29 degreesCf or 12 hours. The seedlings were used for total RNA extraction using RNA easy plant mini kit. Extracted total RNA from the seedlings were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedlings of 12days old of rice (Oryza sativa L. cv Nipponbare) sapk1 mutant was soaked in DW and incubated at 29 degreesCf or 12 hours. SAPK1 are homologue gene in rice for protein kinase gene, ABA-inducible. The seedlings were used for total RNA extraction using RNA easy plant mini kit. Extracted total RNA from the seedlings were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Mutant for protein kinase gene, ABA-inducible, ABA

source_name: Control (CH1) source: The root of 12 days old seedlings

source_name: Target (CH2) source: Seedling (12 days old) of sapk1 mutant


title: 2128_1_C0001_T0003

description:
Control (CH1): Dehusked seeds of rice (Oryza sativa L. cv Nipponbare) were sterilized with 70% ethanol and bleech, germinated and grown with one tenth-strength of MS-salt for 12 days in a plastic tissue culture container under continuous light, treated with water (control). Twelve-day old of wild type seedling was incubated with distiled water for 12 hours under the light condition were used for total RNA preparation by RNA easy plant mini kit. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Dehusked seeds of rice mutant of Osgbf1 mutant (NC6180 on Tos17 database: Oryza sativa L. cv Nipponbare) were sterilized with 70% ethanol and bleech, germinated and grown with one tenth-strength of MS-salt for 12 days in a plastic tissue culture container under continuous light, treated with incubated with 50 micromolar ABA for 12 hours under the light condition. OSGBF are gene for bZIP protein induced by ABA. The twelve-day old for wild type seedling was incubated with distiled water for 12 hours under the light condition were used for total RNA preparation by RNA easy plant mini kit. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Mutant for bZIP protein gene  , ABA

source_name: Control (CH1) source: Twelve-day old wild type seedling

source_name: Target (CH2) source: Seedling of Osgbf1 mutant treated with 50 microM ABA for 12 hours


title: 2123_1_C0001_T0001

description:
Control (CH1): Fully expanded 7th leaf blade of rice (Oryza sativa L. cv Nipponbare: the 8-leaf-stage plants) were used for RNA extraction by Guanidine thiocyanate method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Fully expanded 7th leaf blade of transgenic rice (Oryza sativa L. cv Nipponbare, the 8-leaf-stage plants)  for which overexpressed the Cht-2 (Chitinase-2) gene, were used for RNA extraction by Guanidine thiocyanate method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, Chitinase-2 gene,

source_name: Control (CH1) source: Fully expanded 7th leaf blade of the 8-leaf-stage of nontransgenic plants

source_name: Target (CH2) source: 8-leaf-stage plants overexpressed the Cht-2 gene


title: 2127_2_C0201_T0201

description:
Control (CH1): Callus derived from rice seed (Oryza sativa L. cv Nipponbare) were grown in MS medium with 2,4-D for 24 hours. Then the callus were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Callus derived from rice seed (Oryza sativa L. cv Nipponbare) were grown in MS medium with 2,4-D for 24 hours. The callus were treated with 30 microM 12-oxo-phytodienoic acid (OPDA) for 30 min. Then the callus were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, 12-oxo-phytodienoic acid (OPDA) ,

source_name: Target (CH2) source: Callus treated with 30 microM 12-oxo-phytodienoic acid (OPDA) for 30 min


title: 2128_2_C0001_T0002

description:
Control (CH1): Seedlings of 12days old of rice (Oryza sativa L. cv Nipponbare) was soaked in DW and incubated at 29 degreesCf or 12 hours. The seedlings were used for total RNA extraction using RNA easy plant mini kit. Extracted total RNA from the seedlings were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedlings of 12days old of rice (Oryza sativa L. cv Nipponbare) was soaked in soaked in 50 micromolar ABA for 12 hours and incubated at 29 degreesC for 12 hours. The seedlings were used for total RNA extraction using RNA easy plant mini kit. Extracted total RNA from the seedlings were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, ABA,

source_name: Target (CH2) source: Seedling (12 days old)  treated with 50 microM ABA for 12 hours


title: 2122_2_C0201_T0201

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown on soil. The plant at 4th leaf stage were sprayed with water and maintained at  greenhouse (20-30 degreesC) for 24 hours, then inoculated with rice blast fungus and incubated in dark room for 20 hours at 26 degreesC with 100% humidity. And the plant were transfered to greenhouse (20-30 degreesC) for 22 hours. Then total RNA was extracted, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown on soil. The plant at 4th leaf stage were sprayed with 1mM 1-aminocyclopropane-1-carboxylate (ACC: precursor of ethylene) solution and maintained at  greenhouse (20-30 degreesC) for 24 hours, then inoculated with rice blast fungus and incubated in dark room for 20 hours at 26 degreesC with 100% humidity. And the plant were transfered to greenhouse (20-30 degreesC) for 22 hours. Then total RNA was extracted, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Pathogen, Blast fungus , 1-aminocyclopropane-1-carboxylate(ACC)

source_name: Control (CH1) source: Plant (leaf in 4th leaf stage) grown on soil, sprayed with water (66 hours)

source_name: Target (CH2) source: Leaf infected blast fungus for 20 hours after 1mM 1-aminocyclopropane-1-carboxylate(ACC) treatment


title: 2128_1_C0001_T0002

description:
Control (CH1): Dehusked seeds of rice (Oryza sativa L. cv Nipponbare) were sterilized with 70% ethanol and bleech, germinated and grown with one tenth-strength of MS-salt for 12 days in a plastic tissue culture container under continuous light, treated with water (control). Twelve-day old of wild type seedling was incubated with distiled water for 12 hours under the light condition were used for total RNA preparation by RNA easy plant mini kit. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Dehusked seeds of rice mutant of Osgbf1 mutant (NC6180 on Tos17 database: Oryza sativa L. cv Nipponbare) were sterilized with 70% ethanol and bleech, germinated and grown with one tenth-strength of MS-salt for 12 days in a plastic tissue culture container under continuous light, treated with water. OSGBF are gene for bZIP protein induced by ABA. The twelve-day old for wild type seedling was incubated with distiled water for 12 hours under the light condition were used for total RNA preparation by RNA easy plant mini kit. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Mutant for bZIP protein gene  , ABA

source_name: Target (CH2) source: Seedling of Osgbf1 mutant


title: 2127_1_C0001_T0001

description:
Control (CH1): Callus derived from rice seed (Oryza sativa L. cv Nipponbare) were grown in MS medium with 2,4-D for 24 hours. Then the callus were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Callus derived from rice seed (Oryza sativa L. cv Nipponbare) were grown in MS medium with 2,4-D for 24 hours. The callus were treated with 30 mM methyl jasmonate for 30 min. Then the callus were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Methyl jasmonate ,

source_name: Target (CH2) source: Callus treated with 30 mM methyl jasmonate for 30 min


title: 2125_1_C0001_T0001

description:
Control (CH1): Rice plants (Oryza sativa L. cv. Yukihikari) were grown hydroponically at 25 degrees C under continuous light. Root tissue of the plant at stage of 7-day-old seedlings grown were collected before chilling treatment for RNA extraction by TRIZOL. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice plants (Oryza sativa L. cv. Yukihikari) were grown hydroponically at 25 degrees C under continuous light. Root tissue of the plant at stage of 7-day-old seedlings grown were collected at 2 hours after ransfer to 12 degreesC for RNA extraction by TRIZOL. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, ,

source_name: Control (CH1) source: Root tissues of seedlings collected before chilling treatment

source_name: Target (CH2) source: Root tissues treated with low temperature (12 degrees C, 2 hours)


title: 2117_2_C0101_T0102

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown on 0.8% agar medium with Uniconazole (Uni: 0.1 microM) and Brassinazole (Brz: 1 microM) (continuous light, 27 degreesC ).The seedling, aerial part below lamina joint of second leaf, was used for RNA extraction. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown on 0.8% agar medium with Uniconazole (Uni: 0.1 microM) and Brassinazole (Brz: 1 microM) for 2 days (continuous light, 27 degreesC ).The seedlings treated with BR(Brassinolide: 10ng/plant). Aerial part below lamina joint of second leaf, was used for RNA extraction. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Brassinosteroid,

source_name: Control (CH1) source: Plants (seedling)treated with Uniconazole (Uni: 0.1 microM) and Brassinazole (Brz: 1 microM)

source_name: Target (CH2) source: Seedling (aerial part below lamina joint of second leaf) treated with BR (10ng/plant)


title: 2118_1_C0001_T0001

description:
Control (CH1): 6-month-old suspension culture derived from anther culture of Rice (Oryza sativa L. cv Nipponbare, segregated OSMPK2-wild type) were treated with mock. Messenger RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): 6-month-old suspension culture derived from anther culture of Rice (Oryza sativa L. cv Nipponbare, segregated OSMPK2-wild type) were treated with 1 micro g/mL (GluNAc)7 (heptamer of N-acetyl glucosamin) for 1 hour. Messenger RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Elicitor, Chitin oligomer,

source_name: Control (CH1) source: Callus (pollen) treated with mock

source_name: Target (CH2) source: Callus (from anther culture) treated with 7mer GluNAc (1 micro g/mL of heptamer of N-acetyl glucosamin; chitin) for 1hour


title: 2126_1_C0101_T0101

description:
Control (CH1): Spikelets (5.5 - 6.5 mm long) with young microspores of rice plants {Oryza sativa L. cv. the chilling tolerant near-isogenic line (B5F5) derived from five backcrosses between a recurrent parent 'Toyohikari' (chilling suceptible) and a donor parent 'Hayayuki' (chilling tolerant)} grown at  25/19 degrees C (day/night) for 4 days in phytotron, were harvested at the early microspore stage (11 days before heading). Harvested spikelets were used for RNA extraction by Fast RNA-kit. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Spikelets (5.5 - 6.5 mm long) with young microspores of rice plants {Oryza sativa L. cv. Toyohikari (chilling susceptible at the booting stage), the recurrent parent of the near-isogenic line '510-2' } grown at  12 degreesC for 4 days, were harvested at the early microspore stage (11 days before heading). Harvested spikelets were used for RNA extraction by Fast RNA-kit. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, ,

source_name: Control (CH1) source: Spikelets with young microspores at the early microspore stage (11 days before heading)

source_name: Target (CH2) source: Spikelets with young microspores treated with low temperature (12 degreesC, 4 days)


title: 2121_2_C0201_T0201

description:
Control (CH1): Supension cells (mesocotyl origin) of Bromus inermis Leyss, cv. Manchar cultured in ER medium at 92rpm, inoculated with 2ml cell at 25 degreesC for 7 days. The cell was used for extraction of total RNA by SDS-phenol method. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 mRNA purification kit. Messenger RNA labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Supension cells (mesocotyl origin) of Bromus inermis Leyss, cv. Manchar  cultured in ER medium with 75 microM ABA at 92rpm for 7 days at 25 degreesC, inoculated with 2ml cells. The cell was used for extraction of total RNA by SDS-phenol method. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 mRNA purification kit. Messenger RNA labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, ABA,

organism: Bromus inermis

source_name: Control (CH1) source: Suspension culture (control cells) grown for 7d at 25 degrees C

source_name: Target (CH2) source: Suspension culture cell treated with 75 microM ABA for 7 days


title: 2123_2_C0002_T0004

description:
Control (CH1): Leaf (5th leaf stage) of rice (Oryza sativa L. cv Sasanishiki) were harvested at 24 hours after  inoculation by mock. The leaves were used for RNA extraction by Guanidine thiocyanate method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaf (5th leaf stage) of rice (Oryza sativa L. cv Sasanishiki) were harvested at 24 hours after  inoculation by blast fungus (race 003). The leaves were used for RNA extraction by Guanidine thiocyanate method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Pathogen, Blast fungus ,

source_name: Control (CH1) source: Leaf (5th leaf stage) inoculated by mock, 24 hours after

source_name: Target (CH2) source: Leaf harvested on 24 hour after infection of blast fungus


title: 2115_2_C0201_T0201

description:
Control (CH1): Suspension-cultured cells of the japonica rice variety Nipponbare were derived from embryogenic calli induced on N6 media containing 2,4D at 2 mg/L. Total RNA of the cell were extracted by using SDS-phenol method. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Suspension-cultured cells of the japonica rice variety Nipponbare were derived from embryogenic calli induced on N6 media containing 2,4D at 2 mg/L. Then, cells were treated with chitin (7 mer) for 30 min. Total RNA of the cell were extracted by using SDS-phenol method. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Elicitor, Chitin oligomer,

source_name: Control (CH1) source: Suspension cultuered cell from embryogenic calli (non-treated control cell)

source_name: Target (CH2) source: Suspension-cultured cells treated with elicitor (Chitin 7mer) for 30 min


title: 2123_1_C0001_T0002

description:
Control (CH1): Fully expanded 7th leaf blade of rice (Oryza sativa L. cv Nipponbare: the 8-leaf-stage plants) were used for RNA extraction by Guanidine thiocyanate method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Fully expanded 7th leaf blade of transgenic rice (Oryza sativa L. cv Nipponbare, the 8-leaf-stage plants)  for which overexpressed the Gns-1 (beta-1,3-1,4-glucanase) gene, were used for RNA extraction by Guanidine thiocyanate method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, beta-1,3-1,4-glucanase gene,

source_name: Control (CH1) source: Fully expanded 7th leaf blade of the 8-leaf-stage of nontransgenic plants

source_name: Target (CH2) source: 8-leaf-stage plants overexpressed the Gns1 gene


title: 2123_2_C0004_T0005

description:
Control (CH1): Leaf (5th leaf stage) of rice (Oryza sativa L. cv Sasanishiki) were harvested at 72 hours after  inoculation by mock. The leaves were used for RNA extraction by Guanidine thiocyanate method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaf (5th leaf stage) of rice (Oryza sativa L. cv Sasanishiki) were harvested at 48 hours after  inoculation by blast fungus (race 003). The leaves were used for RNA extraction by Guanidine thiocyanate method. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Pathogen, Blast fungus ,

source_name: Control (CH1) source: Leaf (5th leaf stage) inoculated by mock, 72 hours after

source_name: Target (CH2) source: Leaf harvested on 48 hour after infection of blast fungus


title: 2116_2_C0001_T0003

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) of five-day-old rice seedling after germination was cultivated on filter paper. Five-day-old rice seedling was treated by water for 24 hours. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) of five-day-old rice seedling after germination was cultivated on filter paper. Five-day-old rice seedling was treated with 1 microM Uniconazole P for 24 hours. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Uniconazole P,

source_name: Control (CH1) source: Seedling of five-day-old rice without treatment

source_name: Target (CH2) source: Five-day-old rice seedling treated with 1 microM Uniconazole P for 24 hours


title: 2117_1_C0001_T0002

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown on 0.8% agar medium with Uniconazole (Uni: 0.1 microM) and Brassinazole (Brz: 1 microM) (continuous light, 27 degreesC ).The seedling, aerial part below lamina joint of second leaf, was used for RNA extraction. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown on 0.8% agar medium with Uniconazole (Uni: 0.1 microM) and Brassinazole (Brz: 1 microM) for 2 days (continuous light, 27 degreesC ).The seedlings treated with GA (Gibberellin)+BR(Brassinolide) for 24 hours (10ng/plant in each hormone). aerial part below lamina joint of second leaf, was used for RNA extraction. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, GA, Brassinosteroid

source_name: Control (CH1) source: Plants (leaf) treated with Uniconazole (Uni: 0.1 microM) and Brassinazole (Brz: 1 microM)

source_name: Target (CH2) source: Seedling (aerial part below lamina joint of second leaf) treated with GA+BR (10ng/plant)


title: 2117_2_C0101_T0101

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown on 0.8% agar medium with Uniconazole (Uni: 0.1 microM) and Brassinazole (Brz: 1 microM) (continuous light, 27 degreesC ).The seedling, aerial part below lamina joint of second leaf, was used for RNA extraction. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown on 0.8% agar medium with Uniconazole (Uni: 0.1 microM) and Brassinazole (Brz: 1 microM) for 2 days (continuous light, 27 degreesC ).The seedlings treated with GA (Gibberellin: 10ng/plant). Aerial part below lamina joint of second leaf, was used for RNA extraction. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, GA,

source_name: Control (CH1) source: Plants (seedling)treated with Uniconazole (Uni: 0.1 microM) and Brassinazole (Brz: 1 microM)

source_name: Target (CH2) source: Seedling (aerial part below lamina joint of second leaf) treated with GA (10ng/plant)


title: 2122_2_C0201_T0203

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown on soil. The plant at 4th leaf stage were sprayed with water and maintained at  greenhouse (20-30 degreesC) for 24 hours, then inoculated with rice blast fungus and incubated in dark room for 20 hours at 26 degreesC with 100% humidity. And the plant were transfered to greenhouse (20-30 degreesC) for 22 hours. Then total RNA was extracted, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare IL7: Nipponbare isogenic line with a resitant allele of Pi-i against rice blast fungus) were grown on soil. The plant at 4th leaf stage were sprayed with water and maintained at  greenhouse(20-30 degreesC) for 24 hours, then inoculated with rice blast fungus and incubated in dark room for 20 hours at 26 degreesC with 100% humidity. And the plant were transfered to greenhouse (20-30 degreesC) for 22 hours. Then total RNA was extracted, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Pathogen, Blast fungus ,

source_name: Control (CH1) source: Plant (leaf in 4th leaf stage) grown on soil, sprayed with water

source_name: Target (CH2) source: Leaf infected blast fungus for 20 hours without pretreatment


title: 2122_2_C0001_T0001

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown on soil. The plant at 4th leaf stage were sprayed with water and maintained at  greenhouse 25 degreesC for 24 hours. Then total RNA was extracted, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown on soil. The plant at 4th leaf stage were sprayed  with 1mM 1-aminocyclopropane-1-carboxylate (ACC: precursor of ethylene) solution and maintained at  greenhouse 25 degreesC for 24 hours. Then total RNA was extracted, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Pathogen, 1-aminocyclopropane-1-carboxylate(ACC), Pathogen

source_name: Control (CH1) source: Plant (leaf in 4th leaf stage) grown on soil, sprayed with water (24 hours)

source_name: Target (CH2) source: Leaf sprayed with 1mM 1-aminocyclopropane-1-carboxylate(ACC) solution


title: 2129_1_C0001_T0001

description:
Control (CH1): Barley seeds (Hordeum vulgare L. cv. Ehimehadaka no. 1) were germinated and the seedlings were grown hydroponically, as described previously (Mori and Nishizawa, 1987). The roots of plants were harvested for mRNA extraction. Extracted mRNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Barley seeds (Hordeum vulgare L. cv. Ehimehadaka no. 1) were germinated and the seedlings were grown hydroponically, as described previously (Mori and Nishizawa, 1987). For Fe-deficiency treatment, plants were transferred to culture solution without Fe when the third leaf emerged. After 2-weeks of treatment, the roots of plants were harvested for mRNA extraction. Extracted mRNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Nutrient, Fe-deficient , Barley

organism: Hordeum vulgare

source_name: Control (CH1) source: Seedling (root) grown at hydroponics for 33 days  (normal condition)

source_name: Target (CH2) source: Root (33 days after sowing) treated with Fe-deficient condition for 14days


title: 2122_1_C0101_T0101

description:
Control (CH1): Callus of rice (Oryza sativa L. cv Nipponbare), incubated on MS medium for 10 days at 27 degreesC. Then the callus was shaked with MES buffer (pH5.5) for 3 hours (20-30 degrees C). Total RNA from the cell was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Callus of rice (Oryza sativa L. cv Nipponbare) were incubated on MS medium for 10 days at 27 degreesC, then the cell were shaked with 200 microM ethephone solution (induction reagent for ethylene synthesis) in MES buffer (pH5.5) for 3 hours (20 to 30 degreesC). Total RNA from the cell was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Ethephone, Ethylene

source_name: Control (CH1) source: Callus shaked with MES buffer (pH5.5) for 3 h (20-30 degrees C)

source_name: Target (CH2) source: Callus treated with ethephone solution (200 microM)


title: 2115_1_C0001_T0001

description:
Control (CH1): Suspension-cultured cells of the japonica rice variety Nipponbare were derived from embryogenic calli induced on N6 media containing 2,4D at 2 mg/L. Total RNA of the cell were extracted by using SDS-phenol method. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Suspension-cultured cells of the japonica rice variety Nipponbare were derived from embryogenic calli induced on N6 media containing 2,4D at 2 mg/L. Then, cells were treated with N-acetylchitoheptaose, a potent oligosaccharide elicitor, at 1 micro gram /ml for 30 min at 25 degreesC. Total RNA of the cell were extracted by using SDS-phenol method. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Elicitor, Chitin oligomer,

source_name: Control (CH1) source: Suspension cultuered cell from embryogenic calli (non-treated control cell)

source_name: Target (CH2) source: Suspension-cultured cells (from embryogenic calli) treated with chitin oligomer (8mer) for 30min


title: 2112_1_C0101_T0101

description:
Control (CH1): The japonica rice variety Nipponbare were grown hydroponically, under natural light in a green house. It was 30 degreesC in day,  25 degreesC in night. After growing with deionized water for a week, plants were transfered to hydroponic culture medium (Hayashi and chino 1995) with 1.7mM silicic acid (Si) and further grown for 28days. Total RNA from shoot of the plans was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown hydroponically, under natural light in a green house. It was 30 degreesC in day,  25 degreesC in night. After growing with deionized water for a week, plants were transfered to hydroponic culture medium (Hayashi and chino 1996) without silicic acid (Si) and further grown for 28days. Total RNA from shoot of the plans was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Nutrient, Silicic acid,

source_name: Control (CH1) source: Plants (shoot) grown hydroponically, under natural light in a green house with 1.7mM silicic acid (Si) for 28 days

source_name: Target (CH2) source: Plant (shoot) treated under silicic acid (Si) defecient condition for 28 days


title: 2128_1_C0001_T0001

description:
Control (CH1): Dehusked seeds of rice (Oryza sativa L. cv Nipponbare) were sterilized with 70% ethanol and bleech, germinated and grown with one tenth-strength of MS-salt for 12 days in a plastic tissue culture container under continuous light, treated with water (control). Twelve-day old of wild type seedling was incubated with distiled water for 12 hours under the light condition were used for total RNA preparation by RNA easy plant mini kit. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Dehusked seeds of rice (Oryza sativa L. cv Nipponbare) were sterilized with 70% ethanol and bleech, germinated and grown with one tenth-strength of MS-salt for 12 days in a plastic tissue culture container under continuous light, incubated with 50 micromolar ABA for 12 hours under the light condition. The twelve-day old for wild type seedling was incubated with distiled water for 12 hours under the light condition were used for total RNA preparation by RNA easy plant mini kit. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, ABA,

source_name: Control (CH1) source: Twelve-day old wild type seedling

source_name: Target (CH2) source: Seedling treated with 50 microM ABA for 12 hours


title: 2122_1_C0001_T0001

description:
Control (CH1): Callus of rice (Oryza sativa L. cv Nipponbare), incubated on MS medium for 10 days at 27 degreesC. Total RNA from the cell was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Callus of rice (Oryza sativa L. cv Nipponbare) TEIL (Tobacco EIN-3 like protein) gene was introduced, were incubated on MS medium for 10 days at 27 degreesC. Total RNA from the cell was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, TEIL gene,

source_name: Control (CH1) source: Callus incubated on MS medium for 10 days at 27 degrees C

source_name: Target (CH2) source: Callus introduced with TEIL gene


title: 2111_1_C0001_T0002

description:
Control (CH1): The japonica rice variety Michikogane were grown in 1 mM CaCl2 for 2 days at 28 degrees C (24 hours dark) and in 1 mM CaCl2 for 5 days at 28 degrees C (24 hours light). And then, the plants were transfered in standard nutrient solution containing 1 ppm P for 9 days at 28 degrees C (24 hours light). Root at 5 leaves-stage) of the plants used for total RNA extraction by SDS-phenol method (Wasaki et al. Plant, Cell and Environment 2003, 26, 1515). Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Michikogane were grown in 1 mM CaCl2 for 2 days at 28 degrees C (24 hours dark) and in 1 mM CaCl2 for 5 days at 28 degrees C (24 hours light). And then, the plants were transfered in standard nutrient solution containing 1 ppm P for 8 days at 28 degrees C (24 hours light). Finally, the plants were treated with standard nutrient solution without phosphate (phosphate defecient conditions)  for 24 hours at 28 C (24 h light). Root at 5 leaves-stage) of the plants used for total RNA extraction by SDS-phenol method (Wasaki et al. Plant, Cell and Environment 2003, 26, 1515). Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Nutrient, Phosphate,

source_name: Control (CH1) source: Root (5 leaves stage) grown in standard nutrient solution containing 1 ppm phosphate for 9 days

source_name: Target (CH2) source: Seedlings treated with phosphate deficient condition for 24 hours at 28 degreesC (24 hours light)


title: 2108_1_C0101_T0101

description:
Control (CH1): Triticum aestivum (wheat) variety Valuevskaya were grown at 20/15 degrees C (day/night) with a 15 hours photoperiod. Aerial parts including leaf and stem at the two-leaf stage was used for RNA extraction. RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Triticum aestivum (wheat) variety Valuevskaya were grown at 20/15 degrees C (day/night) with a 15 hours photoperiod. Aerial parts including leaf and stem at the two-leaf stage was treated with low temperature (4 degreesC) for 24 hours, and then used for RNA extraction. RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, Wheat,

organism: Triticum aestivum

source_name: Control (CH1) source: Valuevskaya plant (leaf, seedlings 11d) controled at 20/15 degrees C (day/night) with a 15 hours photope

source_name: Target: Aerial parts including leaf and stem at the two-leaf stage treated with low temperature (4 degreesC) for 24 hours


title: 2110_2_C0002_T0002

description:
Control (CH1): Seedlings of the japonica rice variety Taichung65 germinated under water for two days, then elongation of the seminal root was not inhibited by acid stress pH4.2 for one day, while no crown roots were appeared. T65 being acid-tolerant for elongation of the seminal root at pH4.2, and acid-sensitive at pH4.0, the seedlings at two-day stage after the germination were stressed for one day under hydroponics including 10mM MES-NaOH pH4.2, then the seminal root were dissected to isolate the total RNA by Guanidine chloride method. Total RNA was extract by using Guanidine chloride method. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedling of the japonica rice variety Taichung65 germinated under water for two days, then elongation of the seminal root was inhibited by acid stress pH4.0 for one day, while no crown roots were appeared. T65 being acid-tolerant for elongation of the seminal root at pH4.2, and acid-sensitive at pH4.0, the seedlings at two-day stage after the germination were stressed for one day under hydroponics including 10mM MES-NaOH pH4.0, then the seminal root were dissected to isolate the total RNA by Guanidine-chloride method. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Acidic pH, ,

source_name: Control (CH1) source: Seedling (root) stressed for one day pH4.2 after germination for 2 days

source_name: Target (CH2) source: Seedlings (Taichung 65) were stressed for one day under acidic condition (pH4.0)


title: 2109_1_C0001_T0001

description:
Control (CH1): Young seedlings of the japonica rice variety Akitakomachi, germinated under water (submerged condition) at 30 degrees C, and harvested 1week after the germination for RNA extraction. RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Young seedlings of the japonica rice variety Akitakomachi, germinated under water (submerged condition) at 30 degrees C. And 1week after the germination, the seedlings were transferred under submerged condition at 15 degreesC and kept for 30min. Treated seedlings was  harvested 1week after the germination for RNA extraction.  RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, ,

source_name: Control (CH1) source: Young seedlings, germinated at 30 degrees C under water, 1week after the germination

source_name: Target (CH2) source: Young seedlings transferred to low temperature condition (15 degreesC) for 30min


title: 2121_1_C0001_T0001

description:
Control (CH1): Suspension culture inoculated with 1 g of cells of Bromus inermis Leyss, cv. Manchar grown for 7days at 25 degreesC. The cell was used for extraction of total RNA by SDS-phenol method. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 mRNA purification kit. Messenger RNA labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Supension cells (mesocotyl origin) of Bromus inermis Leyss, cv. Manchar  cultured in ER medium with 75 microM ABA at 92rpm for 7 days at 25 degreesC, inoculated with 2ml cells. The cell was used for extraction of total RNA by SDS-phenol method. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 mRNA purification kit. Messenger RNA labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, ABA,

organism: Bromus secalinus

source_name: Control (CH1) source: Suspension culture (control cells) grown for 7d at 25 degrees C

source_name: Target (CH2) source: Suspension culture cells grown with ABA (75 microM) at 25 degreesC for 7 days


title: 2108_2_C0101_T0102

description:
Control (CH1): Triticum aestivum (wheat) variety Ibis were grown at 20/15 degrees C (day/night) with a 15 hours photoperiod. Aerial parts including leaf and stem at the two-leaf stage was used for RNA extraction. RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Triticum aestivum (wheat) variety  Ibis were grown at 20/15 degrees C (day/night) with a 15 hours photoperiod. Aerial parts including leaf and stem at the two-leaf stage was treated with low temperature (4 degreesC) for 7 days, and then used for RNA extraction. RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, Wheat,

source_name: Control (CH1) source: Ibis plant (shoot, two-leaf stage) controled at 20/15 degrees C (day/night) with a 15 hours photoperiod

source_name: Target (CH2) source: Aerial parts including leaf and stem at the two-leaf stage treated with low temperature (4 degreesC) for 7


title: 2106_2_C0001_T0003

description:
Control (CH1): 50 ml of Oc suspension culture was incubated in MS media by shaking at 26 degrees C for 3 days. mRNA was purified by QuickPrep mRNA purification kit (Pharmacia), labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Suppension culture cells was incubated by shaking at 26 degreesC  for 3 days in the presence of 5-aza cytidine (inhibitor of DNA methylation : 0.3mg/ml). Then, reagent was removed by decantation and the cell was resuspended into fresh media.  Incubation was continued for another 3 days, cell was treated with heat by 42 degreesC for 2 hours. Then total RNA was isolated for the experiment. Messenger RNA was purified by QuickPrep Messenger RNA purification kit (Pharmacia), labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, 5-aza cytidine, Heat shock,

source_name: Control (CH1) source: Suppension culture cells

source_name: Target (CH2) source: Suppension culture cells treated with 5 aza-C and heat


title: 2121_2_C0001_T0001

description:
Control (CH1): Supension cells (mesocotyl origin) of Bromus inermis Leyss, cv. Manchar cultured in ER medium at 92rpm, inoculated with 2ml cell at 25 degreesC for 6 days. The cell was used for extraction of total RNA by SDS-phenol method. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 mRNA purification kit. Messenger RNA labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Supension cells (mesocotyl origin) of Bromus inermis Leyss, cv. Manchar  cultured in ER medium at 92rpm for  6 days (5 days at 25 degreesC and 1 day at 15 degreesC) inoculated with 2ml cells. The cell was used for extraction of total RNA by SDS-phenol method. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 mRNA purification kit. Messenger RNA labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Temperature, ,

source_name: Control (CH1) source: Suspension culture (control cells) grown for 6d at 25 degrees C

source_name: Target (CH2) source: Suspension culture cells treated with low temperature (15 degreesC) for 1 day


title: 2105_2_C0102_T0109

description:
Control (CH1): 15-day-old seedlings (except root) of the japonica rice variety Nipponbare was cultuered in water using Hyponex 10-3-3 (1/1000 dilution) at 28 degrees C (16 hours light, 8 hours dark), and then harvested at 24 hours after  gamma-ray unirradiation (0min)  (= after same actions without gamma-ray irradiation). After harvesting, we used an RNeasy Plant Mini Kit (QIAGEN) to extract total RNA from the plants. Total RNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference.
Target (CH2): 15-day-old seedlings (except root) of the japonica rice variety Nipponbare was cultuered in water using Hyponex 10-3-3 (1/1000 dilution) at 28 degrees C (16 hours light, 8 hours dark), and then harvested at 24 hours after  gamma-ray unirradiation (78.2Gy = 9.2Gy/min x 8.5min). After harvesting, we used an RNeasy Plant Mini Kit (QIAGEN) to extract total RNA from the plants. Total RNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Oxidative, Gamma-ray,

source_name: Control (CH1) source: Seedling of 24 hours after gamma-ray unirradiation (actions without gamma-ray irradiation)

source_name: Target (CH2) source: 15day-old seedlings (except root) after 24 hours of gamma irradiation


title: 2107_2_C0001_T0001

description:
Control (CH1): Leaves at stage of 4th-leaf completely expanded were grown in modified white's medium at 33 degrees C. Then RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaves at stage of 4th-leaf completely expanded of albino-variegated mutant from the japonica rice variety Taichung 65 were grown in modified white's medium at 33 degrees C. Then RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Albino,

source_name: Control (CH1) source: Leaves at stage of 4th-leaf completely expanded of wild type grown in 33 degreesC

source_name: Target (CH2) source: Leaves at stage of 4th-leaf completely expanded of albino-variegated mutant


title: 2106_2_C0001_T0002

description:
Control (CH1): 50 ml of Oc suspension culture was incubated in MS media by shaking at 26 degrees C for 3 days. mRNA was purified by QuickPrep mRNA purification kit (Pharmacia), labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Suppension culture cells 3days after innoculation that were treated with heat (42 degreesC, 2 hours). Messenger RNA was purified by QuickPrep mRNA purification kit (Pharmacia), labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Temperature, Heat shock,

source_name: Target (CH2) source: Suppension culture cells treated with heat (42 degreesC, 2 hours)


title: 2118_2_C0003_T0001

description:
Control (CH1): Insertion mutant (Tos17ID: ND7051) of WRKY gene from Oryza sativa, Nipponbare (segrigated wild-type) was grown at green house for three-month. The leaf were used for RNA extraction. Messenger RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Insertion mutant (Tos17ID: ND7051) of WRKY gene from Oryza sativa, Nipponbare (segrigated wild-type) was grown at green house for three-month.  The plants were incubated for 24 hours on the buffer (0.05%MES/KOH(ph 5.8)) after cutting into sengements. The leaf wounded treatment were used for RNA extraction. Messenger RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, WRKY gene,

source_name: Control (CH1) source: Non treated leaf (three-month in the green house) of insertion mutant of WRKY gene (segrigated wild-type)

source_name: Target (CH2) source: Insertion mutant of WRKY gene (segrigated wild-type) with wounding treatment


title: 2109_2_C0001_T0002

description:
Control (CH1): Seedlings of the japonica rice variety Akitakomachi were grown under submarged condition at 20 degreesC. Coleoptiles at germination stage was harvested for RNA extraction. RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedlings of the japonica rice variety Akitakomachi were grown under submarged condition at 20 degreesC. And then seedlings was cooled down to 15 degrees. the Coleoptiles of seedlings at germination stage was harvested for RNA extraction. RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Anerobic, Cold,

source_name: Control (CH1) source: Seedling (coleoptile) of submarged rice grown at 20 degreesC

source_name: Target (CH2) source: Seedlings (coleoptiles at germination) of submarged plant grown at 20 degreesC, cooled down to 15 degrees


title: 2106_1_C0001_T0001

description:
Control (CH1): 50 ml of Oc suspension culture was incubated in MS media by shaking at 26 degrees C for 3 days. mRNA was purified by QuickPrep mRNA purification kit (Pharmacia), labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): 50 ml of Oc suspension culture was incubated by shaking at 26 degreesC  for 4 days in the presence of 5-aza cytidine (inhibitor of DNA methylation : 0.3mg/ml). Then, reagent was removed by decantation and the cell was resuspended into fresh media.  Incubation was continued for another 3 days, then total RNA was isolated for the experiment. Messenger RNA was purified by QuickPrep mRNA purification kit (Pharmacia), labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, 5-aza cytidine, ,

source_name: Control (CH1) source: Oc suppension cultured cells

source_name: Target (CH2) source: Oc suspension culture treated with 5-aza cytidine (0.3mg/ml) for 4 days


title: 2105_2_C0002_T0009

description:
Control (CH1): 14-day-and-8 hours-old seedlings (except root) of the japonica rice variety Nipponbare was cultuered in water using Hyponex 10-3-3 (1/1000 dilution) at 28 degrees C (16 hours light, 8 hours dark), and then harvested at 8 hours after  gamma-ray unirradiation (0min)  (= after same actions without gamma-ray irradiation). After harvesting, we used an RNeasy Plant Mini Kit (QIAGEN) to extract total RNA from the plants. Total RNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference.
Target (CH2): 14-day-and-8 hours-old seedlings (except root) of the japonica rice variety Nipponbare was cultuered in water using Hyponex 10-3-3 (1/1000 dilution) at 28 degrees C (16 hours light, 8 hours dark), and then harvested at 8 hours after  gamma-ray unirradiation (78.2Gy = 9.2Gy/min x 8.5min). After harvesting, we used an RNeasy Plant Mini Kit (QIAGEN) to extract total RNA from the plants. Total RNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Oxidative, Gamma-ray,

source_name: Control (CH1) source: Seedling of 8 hours after gamma-ray unirradiation ( actions without gamma-ray irradiation)

source_name: Target (CH2) source: 14day-and-8 hours-old seedling (except root) harvested on 8 hours after treatment with gamma ray irradiation


title: 2116_2_C0001_T0002

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) of five-day-old rice seedling after germination was cultivated on filter paper. Five-day-old rice seedling was treated by water for 24 hours. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) of five-day-old rice seedling after germination was cultivated on filter paper. Five-day-old rice seedling was treated with 1 microM GA3 for 24 hours. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, GA,

source_name: Control (CH1) source: Seedling of five-day-old rice without treatment

source_name: Target (CH2) source: Five-day-old rice seedling treated with 1 microM GA3 for 24 hours


title: 2105_1_C0002_T0009

description:
Control (CH1): 14-day-old seedling (except root) of the japonica rice variety Nipponbare was harvested at 1 days after non-irradiation (= after same actions without UVB irradiation). After harvesting, we used an RNeasy Plant Mini Kit (QIAGEN) to extract total RNA from the plants. Total RNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference.
Target (CH2): 14-day-old seedling (except root) of the japonica rice variety Nipponbarewas harvested at 1 days after treatment with UVB irradiation (3.8J/m2/sec) for 4.8min. After harvesting, we used an RNeasy Plant Mini Kit (QIAGEN) to extract total RNA from the plants. Total RNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Oxidative, UV,

source_name: Control (CH1) source: Seedling of 1day after nonirradiation (actions without UVB irradiation)

source_name: Target (CH2) source: 14-day-old seedling (except root) harvested on 1day after treatment with UVB irradiation


title: 2105_1_C0201_T0204

description:
Control (CH1): 16-day-old seedling (except root) of the japonica rice variety Nipponbare was harvested at 3 days after non-irradiation (= after same actions without UVB irradiation). After harvesting, we used an RNeasy Plant Mini Kit (QIAGEN) to extract total RNA from the plants. Total RNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference.
Target (CH2): 16-day-old seedling (except root) of the japonica rice variety Nipponbarewas harvested at 3 days after treatment with UVB irradiation (3.8J/m2/sec) for 4.8min. After harvesting, we used an RNeasy Plant Mini Kit (QIAGEN) to extract total RNA from the plants. Total RNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Oxidative, UV,

source_name: Control (CH1) source: Seedling of 3days after nonirradiation (actions without UVB irradiation)

source_name: Target (CH2) source: 16-day-old seedling (except root) harvested on 3day after treatment with UVB irradiation


title: 2113_2_C0101_T0101

description:
Control (CH1): Rice seed (the japonica rice variety Nipponbare) were spread on a piece of cheesecloth and soaked in tap water for 2 days at 30 degreesC. These water-treated seeds were sown in a plastic box with a commercial soil mixture (Bonsol). The box was submerged in water inside a container and was kept in a growth chamber at 25 degreesC under illumination (9000 lux) of light with 16-h photoperiod.  The 12-day-old rice seedlings were further submerged in water for 1 hours. Total RNA from leaf of the plants (2.5 leaf stage) was extracted by Logemann et al. (1987),  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice seed (the japonica rice variety Nipponbare) were spread on a piece of cheesecloth and soaked in tap water for 2 days at 30 degreesC. These water-treated seeds were sown in a plastic box with a commercial soil mixture (Bonsol). The box was submerged in water inside a container and was kept in a growth chamber at 25 degreesC under illumination (9000 lux) of light with 16-h photoperiod.  The 12-day-old rice seedlings were further submerged in Oryzemate 1.0g/l. After 7 days of treatment with Oryzamate the leaves were harvested for total RNA preparation. Total RNA from leaf of the plants (2.5 leaf stage) was extracted by Logemann et al. (1987),  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Pathogen, Probenazole ,

source_name: Control (CH1) source: Leaf, 2.5 leaf stage with no treatment (control)

source_name: Target (CH2) source: Plant (2.5 leaf stage) treated with probenazole for 1 hour